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Update snapthots and add release notes for MDAnalysis 2.8.0 #398

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Update snapthots and add release notes for MDAnalysis 2.8.0 #398

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34 changes: 34 additions & 0 deletions doc/source/releases.md
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# MDAnalysis Release Notes


## Release 2.8.0 of MDAnalysis

This a minor release of MDAnalysis.

As of this release MDAnalysis is packaged under a [LGPLv3+ license](https://www.gnu.org/licenses/lgpl-3.0.en.html), and all code contributions are provided under the [LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html).

This release supports NumPy 2.0+ and offers backwards compatibility through to NumPy 1.23.2

Supported Python versions:
- 3.10, 3.11, 3.12, 3.13

### Major features

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.8-is-out) for more details.

* The MDAnalysis package license has changed from GPLv3+ to LGPLv3+ and all code contributions are now under LGPLv2.1+
* MDAnalysis now has a brand new guesser API (PR #3753). See the DefaultGuesser class for more information. Please note that default guessing of types and masses will change in MDAnalysis v3.0.
* DSSP analysis `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP) was added.
* An iterative average structure method was added to `analysis.align` based on DOI 10.1021/acs.jpcb.7b11988.
* The TPR reader has been updated to support Gromacs 2024.
* The AnalysisBase class was enhanced through the introduction of a parallelization API (Issue #4158, PR #4304). Various analyses now support parallel computation, including; RMSD, GNMAnalysis, BAT, dihdral calculations, DSSP, and HydrogenBondAnalysis.

### Notable changes / upcoming deprecations

* MMTF support is now deprecated and will be removed in MDAnalysis v3.0. The `fetch_mmtf` method has been disabled as it no longer works.
* MDAnalysis.analysis.hole2 has been moved to its own mdakit ([mdahole2](https://github.com/MDAnalysis/mdahole2)) and will be fully removed from the core library in MDAnalysis v3.0.
* MDAnalysis.analysis.encore has been deprecated in favour of its own mdakit ([mdaencore](https://github.com/MDAnalysis/mdaencore/)) and will be removed in MDAnalysis v3.0.
* MDAnalysis.analysis.waterdynamics has been deprecated in favour of its own mdakit ([waterdynamics](https://github.com/MDAnalysis/waterdynamics)) and will be removed in MDAnalysis v3.0.
* MDAnalysis.analysis.psa has been deprecated in favour of its own mdakit ([PathSimAnalysis](https://github.com/MDAnalysis/pathsimanalysis)) and will be removed in MDAnalysis v3.0.
* The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` kwargs are deprecated for bond guessing during Universe creation.
Instead, pass `("bonds", "angles", "dihedrals")` into `to_guess` or `force_guess` during Universe creation, and the associated `vdwradii`, `fudge_factor`, and `lower_bound` kwargs into `Guesser` creation. Alternatively, if `vdwradii`, `fudge_factor`, and `lower_bound` are passed into `Universe.guess_TopologyAttrs`, they will override the previous values of those kwargs.
* MDAnalysis.topology.guessers and MDAnalysis.topology.tables are deprecated in favour of the new Guessers API and will be removed in MDAnalysis v3.0.
* Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:`Masses`' no_value_label attribute (np.nan).

## Release 2.7.0 of MDAnalysis

This a minor release of MDAnalysis.
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54 changes: 42 additions & 12 deletions doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr
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Expand Up @@ -139,6 +139,12 @@
'',
':ref:`DATA <DATA-format>`, :ref:`GSD <GSD-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
]),
list([
'mass',
'masses',
'',
':ref:`CONFIG <CONFIG-format>`, :ref:`CRD <CRD-format>`, :ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GMS <GMS-format>`, :ref:`GRO <GRO-format>`, :ref:`GSD <GSD-format>`, :ref:`HISTORY <HISTORY-format>`, :ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XML <XML-format>`, :ref:`XPDB <XPDB-format>`, :ref:`XYZ <XYZ-format>`',
]),
list([
'model',
'models',
Expand Down Expand Up @@ -217,6 +223,12 @@
'B-factor',
':ref:`CRD <CRD-format>`, :ref:`MMTF <MMTF-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`XPDB <XPDB-format>`',
]),
list([
'type',
'types',
'',
':ref:`CONFIG <CONFIG-format>`, :ref:`CRD <CRD-format>`, :ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GMS <GMS-format>`, :ref:`GRO <GRO-format>`, :ref:`GSD <GSD-format>`, :ref:`HISTORY <HISTORY-format>`, :ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XML <XML-format>`, :ref:`XPDB <XPDB-format>`, :ref:`XYZ <XYZ-format>`',
]),
list([
'type_index',
'type_indices',
Expand Down Expand Up @@ -319,8 +331,11 @@
'masses': set({
':ref:`CONFIG <CONFIG-format>`',
':ref:`CRD <CRD-format>`',
':ref:`DATA <DATA-format>`',
':ref:`DMS <DMS-format>`',
':ref:`GMS <GMS-format>`',
':ref:`GRO <GRO-format>`',
':ref:`GSD <GSD-format>`',
':ref:`HISTORY <HISTORY-format>`',
':ref:`IN, FHIAIMS <IN-format>`',
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
Expand All @@ -329,7 +344,11 @@
':ref:`PDB, ENT <PDB-format>`',
':ref:`PDBQT <PDBQT-format>`',
':ref:`PQR <PQR-format>`',
':ref:`PSF <PSF-format>`',
':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
':ref:`TPR <TPR-format>`',
':ref:`TXYZ, ARC <TXYZ-format>`',
':ref:`XML <XML-format>`',
':ref:`XPDB <XPDB-format>`',
':ref:`XYZ <XYZ-format>`',
}),
Expand Down Expand Up @@ -408,13 +427,24 @@
'types': set({
':ref:`CONFIG <CONFIG-format>`',
':ref:`CRD <CRD-format>`',
':ref:`DATA <DATA-format>`',
':ref:`DMS <DMS-format>`',
':ref:`GMS <GMS-format>`',
':ref:`GRO <GRO-format>`',
':ref:`GSD <GSD-format>`',
':ref:`HISTORY <HISTORY-format>`',
':ref:`IN, FHIAIMS <IN-format>`',
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
':ref:`MMTF <MMTF-format>`',
':ref:`MOL2 <MOL2-format>`',
':ref:`PDB, ENT <PDB-format>`',
':ref:`PDBQT <PDBQT-format>`',
':ref:`PQR <PQR-format>`',
':ref:`PSF <PSF-format>`',
':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
':ref:`TPR <TPR-format>`',
':ref:`TXYZ, ARC <TXYZ-format>`',
':ref:`XML <XML-format>`',
':ref:`XPDB <XPDB-format>`',
':ref:`XYZ <XYZ-format>`',
}),
Expand All @@ -437,13 +467,13 @@
list([
':ref:`DATA <DATA-format>`',
'LAMMPS data file',
'angles, bonds, charges, dihedrals, impropers',
'angles, bonds, charges, dihedrals, impropers, masses, types',
'',
]),
list([
':ref:`DMS <DMS-format>`',
'DESRES Molecular Structure file',
'atomnums, bonds, chainIDs, charges, names, resnames',
'atomnums, bonds, chainIDs, charges, masses, names, resnames',
'types',
]),
list([
Expand All @@ -461,7 +491,7 @@
list([
':ref:`GSD <GSD-format>`',
'HOOMD GSD file',
'angles, bonds, charges, dihedrals, impropers, names, radii, resnames',
'angles, bonds, charges, dihedrals, impropers, masses, names, radii, resnames, types',
'',
]),
list([
Expand All @@ -479,19 +509,19 @@
list([
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
'LAMMPS ascii dump file',
'masses, types',
'',
'masses',
]),
list([
':ref:`MMTF <MMTF-format>`',
'MMTF file',
'altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors',
'altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors, types',
'masses',
]),
list([
':ref:`MOL2 <MOL2-format>`',
'Tripos MOL2 file',
'bonds, charges, elements, names, resnames',
'bonds, charges, elements, names, resnames, types',
'masses',
]),
list([
Expand All @@ -503,7 +533,7 @@
list([
':ref:`PDBQT <PDBQT-format>`',
'PDBQT file',
'altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors',
'altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors, types',
'masses',
]),
list([
Expand All @@ -515,31 +545,31 @@
list([
':ref:`PSF <PSF-format>`',
'CHARMM, NAMD, or XPLOR PSF file',
'angles, bonds, charges, dihedrals, impropers, names, resnames',
'angles, bonds, charges, dihedrals, impropers, masses, names, resnames, types',
'',
]),
list([
':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
'AMBER topology file',
'angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices',
'angles, bonds, charges, dihedrals, impropers, masses, names, resnames, type_indices, types',
'',
]),
list([
':ref:`TPR <TPR-format>`',
'GROMACS run topology file',
'angles, bonds, chainIDs, charges, dihedrals, elements, impropers, molnums, moltypes, names, resnames',
'angles, bonds, chainIDs, charges, dihedrals, elements, impropers, masses, molnums, moltypes, names, resnames, types',
'',
]),
list([
':ref:`TXYZ, ARC <TXYZ-format>`',
'Tinker file',
'bonds, elements, names',
'bonds, elements, names, types',
'masses',
]),
list([
':ref:`XML <XML-format>`',
'HOOMD XML file',
'angles, bonds, charges, dihedrals, impropers, radii',
'angles, bonds, charges, dihedrals, impropers, masses, radii, types',
'',
]),
list([
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